Validation of Quantitative Trait Loci for Multiple Disease Resistance in Barley Using Advanced Backcross Lines Developed with a Wild Barley

Yun, Song Joong; Gyenis, Laszlo; Bossolini, Eligio; Hayes, Patrick; Matus, Iván; Smith, Kevin P.; Steffenson, Brian J.; Tuberosa, Roberto; Muehlbauer, Gary J.

doi:10.2135/cropsci2005.08-0293

Cited by 50 publications

(42 citation statements)

References 53 publications

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Section: Discussionsupporting

confidence: 91%

“…We also observed that the percentage of introgressed regions ranged widely, with individuals containing 0.79-37.45% wild barley introgression, but the average introgression frequency of 13.55% was relatively consistent with the expectation of 12.5%. Collectively, these results corroborate previous studies (Yun et al 2006;Schnaithmann et al 2014) that showed only minor fluctuations in allele frequency occur when introgressing wild barley genomes.The wild barley AB-NAM exhibits low population structure and low LD Population stratification present in association mapping panels can lead to spurious associations if not appropriately controlled, and effective control of population structure can lower the power to detect marker-trait associations (Larsson et al 2013). The NAM design attempts to eliminate this problem by nesting segments of diverse blocks in a controlled crossing structure (Yu et al 2008).…”

supporting

confidence: 91%

“…To compare genome-wide measures of LD in wild barleyderived mapping populations, genome-wide pairwise marker correlations were calculated using 967 typed or imputed BOPA1 SNP markers that were segregating in each of four populations: (1) the 796 line wild barley AB-NAM described here, (2) the 318 accession WBDC (Steffenson et al 2007), (3) 98 BC 2 F 8 AB lines (HOUH-AB), and (4) 92 RIL lines (HOUH-RIL) derived from the wild barley 3 two-row malting barley cross OUH-602 3 Harrington (Yun et al 2005(Yun et al , 2006. The HOUH-AB and HOUH-RIL populations were genotyped with the same 384-SNP platform used to genotype the AB-NAM.…”

Section: Population Structure and Ldmentioning

confidence: 99%

“…Principal component analysis was performed using the R eigenfunction with and without the parental genotypes included. To reduce the overrepresentation of high LD markers in low recombination regions of the genome, 20 SNPs from the imputed iSelect markers were randomly selected from each 5-cM interval throughout the genome, for a total of 1932 markers used in the analyses.To compare genome-wide measures of LD in wild barleyderived mapping populations, genome-wide pairwise marker correlations were calculated using 967 typed or imputed BOPA1 SNP markers that were segregating in each of four populations: (1) the 796 line wild barley AB-NAM described here, (2) the 318 accession WBDC (Steffenson et al 2007), (3) 98 BC 2 F 8 AB lines (HOUH-AB), and (4) 92 RIL lines (HOUH-RIL) derived from the wild barley 3 two-row malting barley cross OUH-602 3 Harrington (Yun et al 2005(Yun et al , 2006. The HOUH-AB and HOUH-RIL populations were genotyped with the same 384-SNP platform used to genotype the AB-NAM.…”

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confidence: 99%

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Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild × Cultivated Barley

et al. 2016

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The ability to access alleles from unadapted germplasm collections is a long-standing problem for geneticists and breeders. Here we developed, characterized, and demonstrated the utility of a wild barley advanced backcross-nested association mapping (AB-NAM) population. We developed this population by backcrossing 25 wild barley accessions to the six-rowed malting barley cultivar Rasmusson. The 25 wild barley parents were selected from the 318 accession Wild Barley Diversity Collection (WBDC) to maximize allelic diversity. The resulting 796 BC 2 F 4:6 lines were genotyped with 384 SNP markers, and an additional 4022 SNPs and 263,531 sequence variants were imputed onto the population using 9K iSelect SNP genotypes and exome capture sequence of the parents, respectively. On average, 96% of each wild parent was introgressed into the Rasmusson background, and the population exhibited low population structure. While linkage disequilibrium (LD) decay (r 2 = 0.2) was lowest in the WBDC (0.36 cM), the AB-NAM (9.2 cM) exhibited more rapid LD decay than comparable advanced backcross (28.6 cM) and recombinant inbred line (32.3 cM) populations. Three qualitative traits: glossy spike, glossy sheath, and black hull color were mapped with high resolution to loci corresponding to known barley mutants for these traits. Additionally, a total of 10 QTL were identified for grain protein content. The combination of low LD, negligible population structure, and high diversity in an adapted background make the AB-NAM an important tool for highresolution gene mapping and discovery of novel allelic variation using wild barley germplasm.KEYWORDS wild barley; advanced backcross; nested association mapping population; association mapping; plant genetic resources; Multiparent Advanced Generation Inter-Cross (MAGIC); multiparental populations; MPP D IVERSE germplasm collections are valuable resources for crop improvement. However, breeders often neglect these resources due to the time and effort required to identify and deploy beneficial exotic alleles. Breeding for complex traits requires balancing the introduction of genetic diversity with maintaining the selective progress obtained over many cycles of breeding (Bernardo 2002). Due to the malting quality requirements imposed by North American malting and brewing industries, barley (Hordeum vulgare subsp. vulgare) breeding has been restricted to a narrow germplasm base and focused on elite-by-elite crosses (Rasmusson and Phillips 1997). Over many cycles of breeding, extensive genome-wide linkage disequilibrium (LD) can develop in closed breeding populations (Fang et al. 2013), and the genetic diversity of these populations becomes reduced (Condón et al. 2008;Fu and Somers 2009;Muñoz-Amatriaín et al. 2010;Poets et al. 2015). The need to expand the genetic diversity of the breeding pool has become evident as breeders face disease and environmental pressures which are threatening crop production. Today, genomics technologies are advancing our ability to understand the genetic basis of ...

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Section: Discussionsupporting

confidence: 91%

supporting

confidence: 91%

Section: Population Structure and Ldmentioning

confidence: 99%

mentioning

confidence: 99%

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Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild × Cultivated Barley

et al. 2016

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“…Graphical genotypes are used for a number of analyses. Firstly, graphical genotypes can display the positions and the proportions of donor and recurrent genome during subsequent backcross generations (Young and Tanksley, 1989;Yun et al 2006). Secondly, graphical genotypes allow quick data inspection and the visual identification of singletons (Fig.…”

Section: Graphical Genotypingmentioning

confidence: 99%